Strange bone rotation after importing from unity
Just Restating the Answer to this question:

You might want to check the import settings for the armature. You can find it in the bottom left of the import screen. You could try to enable "Ignore Leaf Bones" and "Automatic Bone Orientation". – Ron Deijkers Sep 21 

Please mark this as the best answer for future searches! (All credit to Ron Deijkers BTW).